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Analysis of the Phlebiopsis Gigantea Genome, Transcriptome and Secretome Provides Insight Into Its Pioneer Colonization Strategies of Wood

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Analysis of the Phlebiopsis Gigantea Genome, Transcriptome and Secretome Provides Insight Into Its Pioneer Colonization Strategies of Wood Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood Chiaki Hori1, Takuya Ishida1, Kiyohiko Igarashi1, Masahiro Samejima1, Hitoshi Suzuki2, Emma Master2, Patricia Ferreira3, Francisco J. Ruiz-Duen˜ as4, Benjamin Held5, Paulo Canessa6, Luis F. Larrondo6, Monika Schmoll7, Irina S. Druzhinina8, Christian P. Kubicek8, Jill A. Gaskell9, Phil Kersten9, Franz St. John9, Jeremy Glasner10, Grzegorz Sabat10, Sandra Splinter BonDurant10, Khajamohiddin Syed11, Jagjit Yadav11, Anthony C. Mgbeahuruike12, Andriy Kovalchuk12, Fred O. Asiegbu12, Gerald Lackner13, Dirk Hoffmeister13, Jorge Rencoret14, Ana Gutie´rrez14, Hui Sun15, Erika Lindquist15, Kerrie Barry15, Robert Riley15, Igor V. Grigoriev15, Bernard Henrissat16, Ursula Ku¨ es17, Randy M. Berka18, Angel T. Martı´nez4, Sarah F. Covert19, Robert A. Blanchette5, Daniel Cullen9* 1 Department of Biomaterials Sciences, University of Tokyo, Tokyo, Japan, 2 Department of Chemical Engineering, University of Toronto, Toronto, Ontario, Canada, 3 Department of Biochemistry and Molecular and Cellular Biology and Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Zaragoza, Spain, 4 Centro de Investigaciones Biolo´gicas, Consejo Superior de Investigaciones Cientificas, Madrid, Spain, 5 Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America, 6 Millennium Nucleus for Fungal Integrative and Synthetic Biology and Departamento de Gene´tica Molecular y Microbiologı´a, Facultad de Ciencias Biolo´gicas, Pontificia Universidad Cato´lica de Chile, Santiago, Chile, 7 Health and Environment Department, Austrian Institute of Technology GmbH, Tulin, Austria, 8 Austrian Center of Industrial Biotechnology and Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria, 9 USDA, Forest Products Laboratory, Madison, Wisconsin, United States of America, 10 University of Wisconsin Biotechnology Center, Madison, Wisconsin, United States of America, 11 Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America, 12 Department of Forest Sciences, University of Helsinki, Helsinki, Finland, 13 Department of Pharmaceutical Biology at the Hans-Kno¨ll-Institute, Friedrich-Schiller-University, Jena, Germany, 14 Instituto de Recursos Naturales y Agrobiologia de Sevilla, CSIC, Seville, Spain, 15 US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America, 16 Architecture et Fonction des Macromole´cules Biologiques, Unite´ Mixte de Recherche 7257, Aix-Marseille Universite´, Centre National de la Recherche Scientifique, Marseille, France, 17 Molecular Wood Biotechnology and Technical Mycology, Bu¨sgen-Institute, Georg-August University Go¨ttingen, Go¨ttingen, Germany, 18 Novozymes, Inc., Davis, California, United States of America, 19 Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America Abstract Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh- cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea’s extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes. Citation: Hori C, Ishida T, Igarashi K, Samejima M, Suzuki H, et al. (2014) Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood. PLoS Genet 10(12): e1004759. doi:10.1371/journal.pgen.1004759 Editor: Gregory P. Copenhaver, The University of North Carolina at Chapel Hill, United States of America Received April 15, 2014; Accepted September 16, 2014; Published December 4, 2014 This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Funding: The major portions of this work were performed under US Department of Agriculture Cooperative State, Research, Education, and Extension Service Grant 2007-35504-18257 (to DC and RAB). The US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract DE-AC02-05CH11231. This work was also supported by the HIPOP (BIO2011-26694) project of the Spanish Ministry of Economy and Competitiveness (MINECO) (to FJRD), the PEROXICATS (KBBE-2010-4-265397) and INDOX (KBBE-2013-.3.3-04-613549) European projects (to ATM), and the Chilean National Fund for Scientific and Technological Development Grant 1131030 (to LFL). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * Email: [email protected] PLOS Genetics | www.plosgenetics.org 1 December 2014 | Volume 10 | Issue 12 | e1004759 Phlebiopsis gigantea Colonization of Conifers Author Summary In addition to peroxidases, laccases have been implicated in lignin degradation [24–26]. To date, multiple laccase isozymes The wood decay fungus Phlebiopsis gigantea degrades all and/or the corresponding genes have been characterized from components of plant cell walls and is uniquely able to most white-rot fungi except P. chrysosporium, an efficient rapidly colonize freshly exposed conifer sapwood. Howev- lignocellulose degrader that lacks such enzymes [27–29]. The er, mechanisms underlying its conversion of lignocellulose mechanism(s) by which laccases might degrade lignin remain and resinous extractives have not been explored. We unclear as the enzyme lacks sufficient oxidation potential to cleave report here analyses of the genetic repertoire, transcrip- non-phenolic linkages within the polymer. Interestingly, laccase tome and secretome of P. gigantea. Numerous highly activity has not been reported in P. gigantea. expressed hydrolases, together with lytic polysaccharide Additional ‘auxiliary activities’ [30] commonly ascribed to monooxygenases were implicated in P. gigantea’s attack ligninolytic systems include extracellular enzymes capable of on cellulose, and an array of ligninolytic peroxidases and generating H O . These enzymes may be physiologically coupled auxiliary enzymes were also identified. Comparisons of 2 2 woody substrates with and without extractives revealed to peroxidases. Among them, aryl-alcohol oxidase (AAO), differentially expressed genes predicted to be involved in methanol oxidase (MOX), pyranose 2-oxidase (P2O), and copper the transformation of resin. These expression patterns are radical oxidases (such as glyoxal oxidase, GLX) have been likely key to the pioneer colonization of conifers by P. extensively studied. With the exception of P2O [31], none of gigantea. these activities have been reported in P. gigantea cultures. In short, the repertoire of extracellular enzymes produced by P. Introduction gigantea is largely unknown, and its mechanism(s) for cell wall degradation remain unexplored. The most abundant source of terrestrial carbon is plant biomass, Beyond extracellular systems, the complete degradation of composed primarily of cellulose, hemicellulose, and lignin. lignin requires many intracellular enzymes for the complete Numerous microbes utilize cellulose and hemicellulose, but a mineralization of monomers to CO2 and H2O. Examples of much smaller group of filamentous fungi has the capacity to enzymes that have been characterized from P. chrysosporium degrade lignin, the most recalcitrant component of plant cell walls. include cytochromes P450 (CYPs) [32–34], glutathione transfer- Uniquely, such ‘white-rot’ fungi efficiently depolymerize lignin to ases [35], and aryl alcohol dehydrogenase (AAD) [36]. The role of access cell wall carbohydrates for carbon and energy sources. As such enzymes in P. gigantea, if any, is unknown. such, white-rot fungi play a key role in the carbon cycle. Herein, we report analysis of the P. gigantea draft genome. White-rot basidiomycetes may differ in their substrate prefer- Gene annotation, transcriptome analyses and secretome profiles
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